A fuel cell system that can quickly transition to idling stop and can suppress degradation of the electrolyte membrane and decline in cell voltage during idling stop, without requiring a discharge resistor to be provided, and a control method thereof are provided. A fuel cell system (1) includes a fuel cell (10) configured by layering a plurality of fuel cell cells that generate power by reactant gas being supplied thereto, and a supply device 20 that supplies reactant gas to the fuel cell (10), in which idling stop control is initiated to supply air of a lower flow rate than during idling power generation to the fuel cell (10), while producing lower current than during idling power generation from the fuel cell (10), in a case of a predetermined condition being established during idling power generation.